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Nucleic Acids Research|May 24, 2011
miRvestigator: web application to identify miRNAs responsible for co-regulated gene expression patterns discovered through transcriptome profilingChristopher L Plaisier, J Christopher Bare, Nitin S Baliga
Genome Research|June 30, 2012
A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancersChristopher L Plaisier, Min Pan, Nitin S Baliga
Source Code for Biology and Medicine|July 15, 2010
GTC: A web server for integrating systems biology data with web tools and desktop applicationsDan Tenenbaum, J Christopher Bare, Nitin S Baliga
Molecular Systems Biology|November 24, 2011
Niche adaptation by expansion and reprogramming of general transcription factorsSerdar Turkarslan, David J Reiss, Goodwin Gibbins, et al.
Nucleic Acids Research|April 16, 2015
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organismDavid J Reiss, Christopher L Plaisier, Wei-Ju Wu, et al.
BMC Bioinformatics|November 21, 2007
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applicationsJ Christopher Bare, Paul T Shannon, Amy K Schmid, et al.
BMC Bioinformatics|July 21, 2010
Integration and visualization of systems biology data in context of the genomeJ Christopher Bare, Tie Koide, David J Reiss, et al.
Nucleic Acids Research|November 8, 2014
Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancersJustin Ashworth, Brady Bernard, Sheila Reynolds, et al.
Plos One|September 26, 2014
Inference of expanded Lrp-like feast/famine transcription factor targets in a non-model organism using protein structure-based predictionJustin Ashworth, Christopher L Plaisier, Fang Yin Lo, et al.
BMC Systems Biology|April 17, 2015
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictionsSamuel A Danziger, David J Reiss, Alexander V Ratushny, et al.
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